• Laser & Optoelectronics Progress
  • Vol. 60, Issue 14, 1412004 (2023)
Yongjian Yu1, Yue Wang2、*, Huan Li2, Wenchao Zhou2, Fengfeng Shu2, Ming Gao2、3, and Yihui Wu1、2、**
Author Affiliations
  • 1School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
  • 2Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, Jilin, China
  • 3University of Chinese Academy of Sciences, Beijing 100049, China
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    DOI: 10.3788/LOP230718 Cite this Article Set citation alerts
    Yongjian Yu, Yue Wang, Huan Li, Wenchao Zhou, Fengfeng Shu, Ming Gao, Yihui Wu. Channel-Wise Attention Mechanism Relevant UNet-Based Diffraction-Limited Fluorescence Spot Detection and Localization[J]. Laser & Optoelectronics Progress, 2023, 60(14): 1412004 Copy Citation Text show less
    Overall architecture of our network. (a) Training network; (b) network prediction process; (c) structure of the SE residual module
    Fig. 1. Overall architecture of our network. (a) Training network; (b) network prediction process; (c) structure of the SE residual module
    Algorithm performance under images with different sizes, densities, and SNRs. (a) F1 under different sizes; (b) F1 under different densities; (c) F1 under different SNRs; (d) localization error under different sizes; (e) localization error under different densities; (f) localization error under different SNRs
    Fig. 2. Algorithm performance under images with different sizes, densities, and SNRs. (a) F1 under different sizes; (b) F1 under different densities; (c) F1 under different SNRs; (d) localization error under different sizes; (e) localization error under different densities; (f) localization error under different SNRs
    Prediction for high-density spot images. (a) Fluorescent spot prediction reaching the diffraction limit; (b) prediction based on density image; (c) detection results of each algorithm in the case of 1200 spots per image
    Fig. 3. Prediction for high-density spot images. (a) Fluorescent spot prediction reaching the diffraction limit; (b) prediction based on density image; (c) detection results of each algorithm in the case of 1200 spots per image
    Representative images of datasets and their corresponding prediction
    Fig. 4. Representative images of datasets and their corresponding prediction
    LossF1 /%RMSE /pixelRecall /%Precision /%
    Our loss84.60.545±0.35782.488.4
    AWing loss83.00.564±0.34880.189.0
    BCE loss80.20.539±0.33776.994.0
    Table 1. Performance of SE-Res-UNet using different density map loss functions
    ModelF1 /%RMSE /pixelRecall /%Precision /%Parameter quantity
    SE-Res-UNet(16)84.50.549±0.35682.788.1772539
    SE-Res-UNet(8)84.30.542±0.35481.689.2210271
    Res-UNet(16)83.70.543±0.36983.284.8743311
    Res-UNet(8)83.90.548±0.35481.488.2758531
    SE-UNet(8)84.00.557±0.35181.189.3141615
    UNet(8)83.40.570±0.35181.986.1138003
    Table 2. Performance of different models on vesicle dataset
    SNRSE-Res-UNetdeepBlinkBig-FISH
    F1 /%RMSE /pixelF1 /%RMSE /pixelF1 /%RMSE /pixel
    131.2±13.31.023±0.13433.1±11.61.115±0.0769.6±3.41.036±0.148
    290.2±8.10.620±0.07588.2±8.10.645±0.08366.4±16.10.736±0.108
    398.9±0.60.362±0.02397.8±1.00.385±0.03193.1±2.10.423±0.033
    499.2±0.60.264±0.02898.5±0.90.292±0.03996.9±2.10.350±0.069
    799.3±0.60.151±0.01798.7±0.70.188±0.03898.1±1.40.271±0.075
    Table 3. Detection and localization performances of different algorithms under different SNRs
    DensitySE-Res-UNetdeepBlinkBig-FISH
    F1 /%RMSE /pixelF1 /%RMSE /pixelF1 /%RMSE /pixel
    20099.1±0.500.062±0.004197.0±0.980.296±0.043598.9±0.610.350±0.0715
    40099.0±0.300.066±0.002694.5±0.580.398±0.019397.3±1.100.409±0.0252
    60098.8±0.310.073±0.003791.9±0.700.502±0.025195.8±1.000.442±0.0185
    80098.6±0.350.081±0.004088.7±0.540.590±0.020995.0±1.500.455±0.0414
    100098.3±0.240.096±0.004485.0±0.660.679±0.015277.7±7.790.592±0.0412
    120097.6±0.250.115±0.004781.4±0.560.745±0.010468.3±11.810.702±0.0634
    Table 4. Detection and localization performances of different algorithms under different densities
    DatasetdeepBlinkSE-Res-UNetBig-FISH
    F1 /%RMSE /pixelF1 /%RMSE /pixelF1 /%RMSE /pixel
    SunTag83.00.382±0.28985.40.595±0.26662.80.553±0.298
    Vesicle82.90.577±0.38483.80.531±0.36367.80.654±0.341
    Receptor80.60.512±0.32080.70.471±0.30572.80.519±0.272
    Dense spots90.60.510±0.16798.60.079±0.01790.10.478±0.118
    Table 5. Detection and localization performances of different algorithms on different datasets
    Yongjian Yu, Yue Wang, Huan Li, Wenchao Zhou, Fengfeng Shu, Ming Gao, Yihui Wu. Channel-Wise Attention Mechanism Relevant UNet-Based Diffraction-Limited Fluorescence Spot Detection and Localization[J]. Laser & Optoelectronics Progress, 2023, 60(14): 1412004
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